spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact ti...
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Autor*in:	Pardo, Brenda [verfasserIn] Spangler, Abby Weber, Lukas M. Page, Stephanie C. Hicks, Stephanie C. Jaffe, Andrew E. Martinowich, Keri Maynard, Kristen R. Collado-Torres, Leonardo

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Spatially-resolved transcriptomics Interactive visualization 10x Genomics Visium

Anmerkung:	© The Author(s) 2022

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 23(2022), 1 vom: 10. Juni
Übergeordnetes Werk:	volume:23 ; year:2022 ; number:1 ; day:10 ; month:06

Links:	Volltext

DOI / URN:	10.1186/s12864-022-08601-w

Katalog-ID:	SPR050775235

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520			\|a Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform.
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allfields	10.1186/s12864-022-08601-w doi (DE-627)SPR050775235 (SPR)s12864-022-08601-w-e DE-627 ger DE-627 rakwb eng Pardo, Brenda verfasserin aut spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. Spatially-resolved transcriptomics (dpeaa)DE-He213 Interactive visualization (dpeaa)DE-He213 10x Genomics Visium (dpeaa)DE-He213 Spangler, Abby aut Weber, Lukas M. aut Page, Stephanie C. aut Hicks, Stephanie C. aut Jaffe, Andrew E. aut Martinowich, Keri aut Maynard, Kristen R. aut Collado-Torres, Leonardo (orcid)0000-0003-2140-308X aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 10. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:10 month:06 https://dx.doi.org/10.1186/s12864-022-08601-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 10 06
spelling	10.1186/s12864-022-08601-w doi (DE-627)SPR050775235 (SPR)s12864-022-08601-w-e DE-627 ger DE-627 rakwb eng Pardo, Brenda verfasserin aut spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. Spatially-resolved transcriptomics (dpeaa)DE-He213 Interactive visualization (dpeaa)DE-He213 10x Genomics Visium (dpeaa)DE-He213 Spangler, Abby aut Weber, Lukas M. aut Page, Stephanie C. aut Hicks, Stephanie C. aut Jaffe, Andrew E. aut Martinowich, Keri aut Maynard, Kristen R. aut Collado-Torres, Leonardo (orcid)0000-0003-2140-308X aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 10. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:10 month:06 https://dx.doi.org/10.1186/s12864-022-08601-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 10 06
allfields_unstemmed	10.1186/s12864-022-08601-w doi (DE-627)SPR050775235 (SPR)s12864-022-08601-w-e DE-627 ger DE-627 rakwb eng Pardo, Brenda verfasserin aut spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. Spatially-resolved transcriptomics (dpeaa)DE-He213 Interactive visualization (dpeaa)DE-He213 10x Genomics Visium (dpeaa)DE-He213 Spangler, Abby aut Weber, Lukas M. aut Page, Stephanie C. aut Hicks, Stephanie C. aut Jaffe, Andrew E. aut Martinowich, Keri aut Maynard, Kristen R. aut Collado-Torres, Leonardo (orcid)0000-0003-2140-308X aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 10. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:10 month:06 https://dx.doi.org/10.1186/s12864-022-08601-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 10 06
allfieldsGer	10.1186/s12864-022-08601-w doi (DE-627)SPR050775235 (SPR)s12864-022-08601-w-e DE-627 ger DE-627 rakwb eng Pardo, Brenda verfasserin aut spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. Spatially-resolved transcriptomics (dpeaa)DE-He213 Interactive visualization (dpeaa)DE-He213 10x Genomics Visium (dpeaa)DE-He213 Spangler, Abby aut Weber, Lukas M. aut Page, Stephanie C. aut Hicks, Stephanie C. aut Jaffe, Andrew E. aut Martinowich, Keri aut Maynard, Kristen R. aut Collado-Torres, Leonardo (orcid)0000-0003-2140-308X aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 10. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:10 month:06 https://dx.doi.org/10.1186/s12864-022-08601-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 10 06
allfieldsSound	10.1186/s12864-022-08601-w doi (DE-627)SPR050775235 (SPR)s12864-022-08601-w-e DE-627 ger DE-627 rakwb eng Pardo, Brenda verfasserin aut spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. Spatially-resolved transcriptomics (dpeaa)DE-He213 Interactive visualization (dpeaa)DE-He213 10x Genomics Visium (dpeaa)DE-He213 Spangler, Abby aut Weber, Lukas M. aut Page, Stephanie C. aut Hicks, Stephanie C. aut Jaffe, Andrew E. aut Martinowich, Keri aut Maynard, Kristen R. aut Collado-Torres, Leonardo (orcid)0000-0003-2140-308X aut Enthalten in BMC genomics London : BioMed Central, 2000 23(2022), 1 vom: 10. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:23 year:2022 number:1 day:10 month:06 https://dx.doi.org/10.1186/s12864-022-08601-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 10 06
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author	Pardo, Brenda
spellingShingle	Pardo, Brenda misc Spatially-resolved transcriptomics misc Interactive visualization misc 10x Genomics Visium spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
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topic_title	spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data Spatially-resolved transcriptomics (dpeaa)DE-He213 Interactive visualization (dpeaa)DE-He213 10x Genomics Visium (dpeaa)DE-He213
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title	spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
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title_full	spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
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author_browse	Pardo, Brenda Spangler, Abby Weber, Lukas M. Page, Stephanie C. Hicks, Stephanie C. Jaffe, Andrew E. Martinowich, Keri Maynard, Kristen R. Collado-Torres, Leonardo
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title_sort	spatiallibd: an r/bioconductor package to visualize spatially-resolved transcriptomics data
title_auth	spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
abstract	Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. © The Author(s) 2022
abstractGer	Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. © The Author(s) 2022
abstract_unstemmed	Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD. It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform. © The Author(s) 2022
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title_short	spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
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fullrecord_marcxml	<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">SPR050775235</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20230509102536.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">230507s2022 xx \|\|\|\|\|o 00\| \|\|eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1186/s12864-022-08601-w</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)SPR050775235</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(SPR)s12864-022-08601-w-e</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Pardo, Brenda</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2022</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">© The Author(s) 2022</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. 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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

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